What ZFIN does

ZFIN (Zebrafish Model Organism Database) is a non-profit, open-access scientific database that serves as the central genetic, genomic, and bibliographic resource for the international zebrafish research community. Established in 1994 and hosted at the University of Oregon, ZFIN curates and disseminates detailed information on zebrafish genes, alleles, mutants, transgenic lines, expression patterns, phenotypes, and the published literature, with the database currently encompassing over 37,970 genes, 67,936 publications, 511,681 expression patterns, and 275,624 phenotype statements. The platform provides free, public access to a web-based query interface, gene pages, downloadable datasets, and nomenclature authority services, and is integrated with the Alliance of Genome Resources for cross-species comparative genomics. The resource is sustained by NIH grant funding and operated by a small team (1-10 employees), with no commercial revenue, subscription fees, or licensing model — ZFIN is a public-good research infrastructure, not a commercial product. It holds the Global Core Biodata Resource designation and partners with the zebrafish stock centers (ZIRC, CZRC, EZRC) and the International Zebrafish Society, serving 11,186+ researchers across 1,867+ labs and 286+ companies worldwide.

Name

ZFIN

Legal name

ZFIN The Zebrafish Information Network (University of Oregon)

Website

https://zfin.org

Company type

Private

Founded year

1994

Operating status

Operating

Headcount range

1–10 employees

Short description

ZFIN is a non-profit, NIH-funded open-access database founded in 1994 and hosted at the University of Oregon that curates zebrafish genetic, genomic, and bibliographic data for the global research community, serving thousands of labs and companies free of charge.

Ownership category

akta.pro rank

Product category

Model Organism Bioinformatics Database

akta.pro primary industry

Knowledge Management & Scientific Collaboration / Literature Intelligence (HLAGAJAN)

Keywords

• Model organism database
• Genomic data curation
• Zebrafish bioinformatics
• Scientific research database
• Genome browsing tools

Headquarters

HQ city

Eugene

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Operations, Infrastructure

Revenue model

1. Grant Funding: ZFIN is funded through institutional grants, primarily from the National Institutes of Health (NIH) and other research funding bodies. The database operates as a non-commercial scientific resource affiliated with the University of Oregon.

Go-to-market motion1 record

Distribution channels3 records

Marketing channels4 records

Core offering

ZFIN (The Zebrafish Information Network) is a web-based, expert-curated database of genetic and genomic data for the zebrafish (Danio rerio) model organism. It provides organized and cross-referenced research data including genes, mutants, transgenic lines, expression patterns, phenotypes, anatomical ontology, and publications, alongside integrated search, BLAST, genome browsing, and data mining tools for the international research community.

Product overview

ZFIN (The Zebrafish Information Network) is a comprehensive database platform providing expert-curated genetic and genomic data for zebrafish (Danio rerio) as a model organism. The platform consists of the core ZFIN Database combined with multiple search interfaces (Gene Search, Expression Search, Mutants/Tg Search, Antibody Search, Anatomy/GO/Human Disease Search, Publications Search), genomics tools (BLAST, JBrowse Genome Browser), data mining platforms (AllianceMine, BioMart), and resource access services (ZIRC ordering, The Zebrafish Book, Data Submissions Portal). The system enables researchers to search, browse, and download curated zebrafish research data across genes, phenotypes, expression patterns, antibodies, anatomy, and publications.

Differentiator

Problem solved

Functional benefit

Products and services

• ZFIN Database Expert-curated database of genetic and genomic data for zebrafish (Danio rerio) as a model organism, providing organized and cross-referenced research data on genes, mutants, expression patterns, phenotypes, and anatomical ontology for the international scientific research community.
• BLAST Sequence Alignment Tool Sequence alignment tool for aligning nucleotide and protein sequences with zebrafish datasets, available through ZFIN and linked to Ensembl, NCBI, and UCSC BLAST services.
• JBrowse Genome Browser Web-based genome browser (JBrowse2) for visualizing zebrafish genomic data and annotations with customizable tracks for gene models, reference sequences, and expression data.
• AllianceMine Data Mining Platform Data mining tool integrated with ZFIN for querying combined data from Alliance of Genome Resources member databases, enabling cross-species comparative genomics research.
• BioMart Data Mining Integration Integration with Ensembl BioMart for cross-database data queries and data export, enabling researchers to query and retrieve zebrafish data alongside other model organism datasets.
• The Zebrafish Book Comprehensive guide for laboratory use of zebrafish (Danio rerio), available as a reference resource covering husbandry, genetics, and experimental methods.
• Data Submissions Portal Guidelines and forms for researchers to submit experimental data to ZFIN for expert curation and inclusion in the database, enabling community contributions.
• ZFIN Nomenclature Service Official zebrafish nomenclature authority service, providing nomenclature conventions, line designations, wild-type lines registry, and submissions for proposed gene and mutant line names.

Quantifiable outcome

• Over 67,900 scientific publications cite ZFIN data, demonstrating the database's central role in zebrafish research
• +2 more outcomes

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration6 records

Feature6 records

Partnerships

Seven partnerships are on record, tiered core and minor.

• Alliance of Genome ResourcescoreTechnology or IntegrationZFIN is a founding member and active contributor to the Alliance of Genome Resources, a consortium that integrates genetic and genomic data from multiple model organisms (human, mouse, zebrafish, fly, worm, yeast, rat). ZFIN provides zebrafish-specific data and participates in cross-species comparative genomics initiatives through this partnership.
• Zebrafish International Resource Center (ZIRC)coreTechnology or IntegrationZIRC is a repository and distribution center for zebrafish lines, cDNA/EST clones, and other biological reagents. ZFIN maintains links to ZIRC enabling researchers to order materials referenced in the database. The organizations are complementary, with ZFIN providing data and ZIRC providing physical resources.
• China Zebrafish Resource Center (CZRC)coreTechnology or IntegrationCZRC provides zebrafish resources and services to the Chinese research community. ZFIN maintains links to CZRC for researchers to access region-specific zebrafish resources and services.
• European Zebrafish Resource Center (EZRC)coreTechnology or IntegrationEZRC provides zebrafish resources and services to the European research community. ZFIN maintains links to EZRC for researchers to access region-specific zebrafish resources and services.
• International Zebrafish Society (IZFS)coreStrategic or Co-development PartnerIZFS is the primary professional society for the zebrafish research community. ZFIN collaborates with IZFS on community events, conferences, and standards initiatives. ZFIN staff participate in IZFS activities and the society promotes ZFIN resources to members.
• Zebrafish Disease Models Society (ZDMS)minorStrategic or Co-development PartnerZDMS focuses on zebrafish as a model for human diseases. ZFIN supports this community by providing disease model data and cross-references to human disease phenotypes.
• University of OregoncoreOthersZFIN is hosted and operated by the University of Oregon, which provides institutional infrastructure, administrative support, and serves as the employer for ZFIN staff.

Scale indicators11 records

Recent moves5 records

Expansion highlights5 records

Broad incumbents

• NCBI Gene / Genome Data Viewer: NCBI's Genome Data Viewer and Gene database provide broad cross-species genomic data including zebrafish. As a federal generalist platform, it competes for researcher attention with ZFIN but lacks the deep, expert-curated phenotype and expression focus.
• Ensembl: Ensembl is a broad, EMBL-EBI-operated genome browser and annotation platform covering dozens of species including zebrafish. It overlaps with ZFIN in genome browsing and BLAST functionality but is a horizontal, multi-species platform rather than a zebrafish specialist.
• UCSC Genome Browser: UCSC Genome Browser provides a multi-species genome visualization platform including zebrafish assemblies. It is comparable to ZFIN's JBrowse integration but operates as a horizontal, broadly-used academic bioinformatics resource rather than a model-organism specialist.

Direct peers

• Xenbase: Xenbase is the primary curated database for Xenopus (frog) genomic and developmental data. It is a directly comparable model organism database serving a vertebrate developmental biology community with significant overlap with ZFIN's zebrafish researcher base.
• MGI (Mouse Genome Informatics): Mouse Genome Informatics is the analog model organism database for the laboratory mouse at the Jackson Laboratory, providing curated genetic, genomic, and phenotype data. It is directly comparable to ZFIN as a community-curated, NIH-funded model organism database serving biomedical researchers.
• FlyBase: FlyBase is the primary curated database for Drosophila melanogaster genetics and genomics, operated as a consortium of universities. Like ZFIN, it serves a model-organism research community, integrates with Alliance of Genome Resources, and provides nomenclature authority and bioinformatics tools.
• WormBase: WormBase is the curated genetic and genomic database for C. elegans, also a member of the Alliance of Genome Resources. It mirrors ZFIN's structure: NIH-funded, expert-curated, free public access, integrated genome browsing, and community nomenclature standards.
• Saccharomyces Genome Database (SGD): SGD is the primary curated resource for Saccharomyces cerevisiae (yeast) genetic and genomic data and an Alliance of Genome Resources member. It is functionally analogous to ZFIN in scope, funding model, and scientific role for its respective model organism community.
• Rat Genome Database (RGD): RGD provides curated genetic, genomic, and phenotype data for the laboratory rat and is also an Alliance of Genome Resources member. It is directly comparable in mission, structure, and target community to ZFIN, serving mammalian model organism researchers.

Emerging players

• Alliance of Genome Resources: The Alliance of Genome Resources is a consortium of which ZFIN is a founding member, integrating model organism databases across species. It represents both a partner and a potential competitive layer that could subsume aspects of ZFIN's individual-database value proposition.

Market position

Strengths4 records

Weaknesses4 records

Competitive moat5 records

Key risks5 records

Key highlights5 records

Customer concentration

• LinkedInlinkedin.com/company/zfin

Revenue estimate

Valuation estimate

Number of profiles

Funding overview

Funding rounds

Investors

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M&A

Investments

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Frequently asked questions about ZFIN